Mercurial > repos > swebb > pycrac

comparison pyCRAC/pyFastqSplitter.xml @ 0:19b20927172d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author swebb
date Tue, 18 Jun 2013 09:11:00 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:19b20927172d
1 <tool id ="pyFastqSplitter" name="pyFastqSplitter" force_history_refresh="True">
2 <requirements>
3 <requirement type="package">pyCRAC</requirement>
4 </requirements>
5 <command interpreter="perl">
6 pyFastqSplitter.pl
7 -f $f
8 --o1 $out1
9 --id $label.value
10 --o2 $out2
11 --file_type $ftype.type
12 #if $joinc.ch == "-c":
13 -c $joinc.c
14 #end if#
15 </command>
16 <version_command>/usr/local/bin/pyFastqSplitter.py --version</version_command>
17 <inputs>
18 <conditional name="ftype">
19 <param name="type" type="select" label="File type">
20 <option value="fastq" selected="true">FASTQ</option>
21 <option value="fasta">FASTA</option>
22 </param>
23 <when value="fastq">
24 <param format="fastq" name="f" type="data" label="FastQ File -f" help="FastQ format" />
25 </when>
26 <when value="fasta">
27 <param format="fasta" name="f" type="data" label="FastA File -f" help="FastA format" />
28 </when>
29 </conditional>
30 <conditional name="joinc">
31 <param name="ch" type="select" label="Insert a character at join">
32 <option value="" selected="true">NO</option>
33 <option value="-c">YES</option>
34 </param>
35 <when value="-c">
36 <param type="text" name="c" label="Split the reads on the -c character" value=":" >
37 <validator type="empty_field" message="enter a character or turn this option off" />
38 </param>
39 </when>
40 <when value="">
41 </when>
42 </conditional>
43 <param name="label" type="text" format="txt" size="30" value="pyFastqSplitter" label="Enter output file label -o" />
44 </inputs>
45 <outputs>
46 <data format="input" name="out1" label="${label.value}_1.${ftype.type}"/>
47 <data format="input" name="out2" label="${label.value}_2.${ftype.type}"/>
48 <change_format>
49 <when input="ftype.type" value="fasta" format="fasta" />
50 </change_format>
51 </outputs>
52 <help>
53
54 .. class:: infomark
55
56 **pyFastqSplitter**
57
58 pyFastqSplitter is part of the pyCRAC_ package. Splits a merged fastq file (pyFastqJoiner output) in to two files.
59
60 Example::
61
62 Here the ":" character was used to separate the two sequences. By using the -c flag you can tell pyFastqSplitter where to split the sequences.
63 This character is ignored by pyFastqDuplicateRemover
64
65
66 @FCC102EACXX:3:1101:1343:2181#ATCACGAT/1##CAATAG@FCC102EACXX:3:1101:1343:2181#ATCACGAT/2
67 CAAATTAGAGTGTTCAAAGCAGGCGTATTGCTCGAAT:AGCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAGA
68 +
69 `efhYb][bdQQ`eeaeaYbeY^ceU__IXa[^ZYaeYJaSJ`Z`K`YbSb[[daeJRR[YeWd_I^I^ecgc]OV\bdeaegbXb
70 @FCC102EACXX:3:1101:1424:2248#ATCACGAT/1##CCAGGA@FCC102EACXX:3:1101:1424:2248#ATCACGAT/2
71 CTAACCATAAACTATGCCTACTAGGGATCCAGAGGTG:AAGTCCTTTAAGTTACAGCCTTGCGACCATACTACACCCAGAACCCAAA
72 +
73 ^_adddhJbaehbedd`dIb_^cXaRI^BBBBBBBBBYJJ\`JQY\`KJ`gY[[QRYY[[`H[_ceI^e[PYO^IWOHW^eaefhh
74 @FCC102EACXX:3:1101:1623:2036#ATCACGAN/1##CTCAGC@FCC102EACXX:3:1101:1623:2036#ATCACGAN/2
75 CAAAGTTAGGGGATCGAAGATGATCAGATACCGTCGT:GGCCAATCCTTATTGTGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTC
76 +
77 bghfc^YbgbeadggfdffeaS^ac_X^cegaGZ_efPP\`ccQ`eY[bQQ[d`ghehaghfgdg[`gb^bd[ePbH^c_c\a_eg
78
79 Result:
80
81 Forward reaction:
82
83 @FCC102EACXX:3:1101:1343:2181#ATCACGAT/1##CAATAG
84 CAAATTAGAGTGTTCAAAGCAGGCGTATTGCTCGAAT
85 +
86 `efhYb][bdQQ`eeaeaYbeY^ceU__IXa[^ZYae
87 @FCC102EACXX:3:1101:1424:2248#ATCACGAT/1##CCAGGA
88 CTAACCATAAACTATGCCTACTAGGGATCCAGAGGTG
89 +
90 ^_adddhJbaehbedd`dIb_^cXaRI^BBBBBBBBB
91 @FCC102EACXX:3:1101:1623:2036#ATCACGAN/1##CTCAGC
92 CAAAGTTAGGGGATCGAAGATGATCAGATACCGTCGT
93 +
94 bghfc^YbgbeadggfdffeaS^ac_X^cegaGZ_ef
95 @FCC102EACXX:3:1101:1574:2214#ATCACGAT/1##CGTTTT
96 CTAATGACCCACTCGGCACCTTACGAAATCAAAGTCT
97 +
98 cdfgYY`cefhhZef\eaggXaceeghfQaeghWNW\
99
100 Reverse reaction:
101
102 @FCC102EACXX:3:1101:1343:2181#ATCACGAT/2
103 AGCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAGA
104 +
105 YJaSJ`Z`K`YbSb[[daeJRR[YeWd_I^I^ecgc]OV\bdeaegbXb
106 @FCC102EACXX:3:1101:1424:2248#ATCACGAT/2
107 AAGTCCTTTAAGTTACAGCCTTGCGACCATACTACACCCAGAACCCAAA
108 +
109 YJJ\`JQY\`KJ`gY[[QRYY[[`H[_ceI^e[PYO^IWOHW^eaefhh
110 @FCC102EACXX:3:1101:1623:2036#ATCACGAN/2
111 GGCCAATCCTTATTGTGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTC
112 +
113 PP\`ccQ`eY[bQQ[d`ghehaghfgdg[`gb^bd[ePbH^c_c\a_eg
114
115 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
116
117 ------
118
119 **Parameter list**
120
121 Options::
122
123 -f fastq_file, --filename=fastq_file
124 To provide the names of two raw data files separated
125 by a single space. Default = standard input
126 --file_type=FASTQ
127 Can split joined fasta and fastq files. Fastq is default
128 If there isn't a specific character splitting the two reads
129 the tool assumes that the two reads were of equal length
130 -o splitfastq, --outfile=splitfastq
131 Provide the name of the output files (WITHOUT file
132 extension). By default the data will be printed to the
133 standard output
134 -c :, --character=:
135 If the joined sequences were separated by a specific
136 character then the program can divide the sequences by
137 looking for that character
138
139 </help>
140 </tool>